hyraxAbif: Modules for parsing, generating and manipulating AB1 files.

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This library provides functionality for parsing, modifying, writing and generating ABIF files

Any AB1 file conforming to the standard at http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf should be supported.

This library also support generating a minimal ABIF file from a FASTA input sequence.

A basic terminal application that can dump and generate AB1s is included. See https://github.com/hyraxbio/hyraxAbif/blob/master/app/Main.hs


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Change logNone available
Dependenciesbase (>= && <5), binary (>= && <, bytestring (>= && <, directory (>= && <, filepath (>= && <, hscolour (>=1.24.4 && <1.25.0), hyraxAbif, pretty-show (>=1.6.16 && <1.7.0), protolude (==0.2.2.*), text (>= && < [details]
Copyright2018 HyraxBio
Maintainerandre@hyraxbio.co.za, andre@andrevdm.com
Home pagehttps://github.com/hyraxbio/hyraxAbif/#readme
Source repositoryhead: git clone https://github.com/hyraxbio/hyraxAbif
UploadedTue Jul 10 08:10:59 UTC 2018 by andrevdm




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Readme for hyraxAbif-

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HyraxBio AB1 parser, writer and generator (beta 0.2)

This project contains



Build with one of

Terminal app

Run with

Dump AB1

To dump an existing AB1 run

hyraxAbif-exe dump example.ab1

This will output the structure of the AB1 like this

Header { hName = "ABIF" , hVersion = 101 }
  { dTagName = "tdir"
  , dTagNum = 1
  , dElemTypeCode = 1023
  , dElemTypeDesc = "root"
  , dElemType = ElemRoot
  , dElemSize = 28
  , dElemNum = 13
  , dDataSize = 364
  , dDataOffset = 61980
  , dData = ""
  , dDataDebug = []
[ Directory
    { dTagName = "DATA"
    , dTagNum = 9
    , dElemTypeCode = 4
    , dElemTypeDesc = "short"
    , dElemType = ElemShort
    , dElemSize = 2
    , dElemNum = 7440
    , dDataSize = 14880
    , dDataOffset = 128
    , dData = ""
    , dDataDebug = []

DATA {short} tagNum=9 size=2 count=7440 offset=128  []
DATA {short} tagNum=10 size=2 count=7440 offset=15008  []
DATA {short} tagNum=11 size=2 count=7440 offset=29888  []
DATA {short} tagNum=12 size=2 count=7440 offset=44768  []
FWO_ {char} tagNum=1 size=1 count=4 offset=1195463747  ["GATC"]
LANE {short} tagNum=1 size=2 count=1 offset=65536  ["1"]
PDMF {pString} tagNum=1 size=1 count=23 offset=60392  ["KB_3500_POP7_BDTv3.mob"]
PDMF {pString} tagNum=2 size=1 count=23 offset=60415  ["KB_3500_POP7_BDTv3.mob"]
PLOC {short} tagNum=1 size=2 count=744 offset=60438  []
S/N% {short} tagNum=1 size=2 count=4 offset=61926  []
SMPL {pString} tagNum=1 size=1 count=10 offset=61934  ["S17-SeqF1"]
CMNT {pString} tagNum=1 size=1 count=1 offset=61944  ["Generated by HyraxBio AB1 generator"]

The data is output twice. The first section is the detail, the second is the summary.

Selected data types have the "debug data" element populated. e.g. the PBAS (FASTA)

Generate minimal AB1s from FASTAs

To create an AB1 run

hyraxAbif-exe gen "./pathContainingFastas" "./pathForOutputAb1s"

This will create an AB1 per input FASTA

Input FASTA format

Each input data should have the following format

> weight
> weight

Weighted reads

For example

> 0.5
> 0.3
> 1

Results in the following weighted nucleotide per position

Note that the reads do not need to be the same length.

Example FASTA - single file


> 1

Here there is a single FASTA with a single read with a weigh of 1 (100%). The chromatogram for this AB1 shows perfect traces for the input ACTG nucleotides

Example FASTA - two FASTA files


> 1


> 1

Two input FASTA files both with a weigh of 1. You can see in the second trace that the third nucleotide is a T (the trace is green). Exactly what the base-calling software (phred & recall etc) decide to call the base as depends on your settings and software choices.

Example FASTA - two FASTA files with different weights


> 1


> 0.3

Here the second fasta has a weight of 0.3 and you can see the traces are 30% of the height of the top ones.

Example FASTA - single FASTA with a mix


> 1
> 0.3

The single input FASTA has an AT mix at the third nucleotide. The first read has a weight of 1 and the second a weight of 0.3. Notice that the maximum weight is 1, e.g. the first A has the same intensity as the second even though the first one has the reads weighted both 1 and 0.3

Example FASTA - Multiple mixes


> 1
> 0.3
> 0.2

Using the modules

For a detailed overview of the code see TODO and the haddock documentation TODO

For now the terminal app (Main.hs) serves as an example and the best starting point to understand the code

E.g. Add a comment to an existing AB1 file

import qualified Hyrax.Abif as H
import qualified Hyrax.Abif.Read as H
import qualified Hyrax.Abif.Write as H

addComment :: IO ()
addComment = do
  abif' <- H.readAbif "example.ab1"

  case abif' of
    Left e -> putText $ "error reading ABIF: " <> e
    Right abif -> do
      let modified = H.addDirectory abif $ H.mkComment "new comment"
      H.writeAbif "example.modified.ab1" modified

For additional examples see the Examples directory